How to make one clear object invisible inside of another clear object?
There is a trick that worked very well for me:

You can make the object "invisible" inside of the clear sphere by adding another sphere just slightly smaller inside of it, adding a Boolean modifier to both the water inside the sphere, and itself. Then set the Boolean sphere to fully transparent so you do not see it. Now the water inside of the sphere should have disappeared. Make sure you do not apply the modifier at all, as that would apply it to the vertices, and change the simulation.